| Previous changeset 1:9e6e840d6b52 (2016-08-08) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 |
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modified:
idconvert.xml |
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removed:
msconvert_macros.xml tool_dependencies.xml |
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| diff -r 9e6e840d6b52 -r edb33e8224c6 idconvert.xml --- a/idconvert.xml Mon Aug 08 10:43:52 2016 -0400 +++ b/idconvert.xml Sat Feb 23 06:21:11 2019 -0500 |
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| @@ -1,9 +1,8 @@ <tool id="idconvert" name="idconvert" version="@VERSION@.0"> <description>Convert mass spectrometry identification files</description> - <macros> - <import>msconvert_macros.xml</import> - </macros> - <expand macro="generic_requirements" /> + <requirements> + <requirement type="package" version="3.0.9992">proteowizard</requirement> + </requirements> <stdio> <exit_code range="1:" /> <regex match="Error" @@ -15,15 +14,15 @@ <![CDATA[ #import os.path #set $input_name = '.'.join([$os.path.basename(str($from.input)),str($from.input.extension).replace('xml','.xml')]) -ln -s "$from.input" "$input_name" && -idconvert $input_name +ln -s '$from.input' '$input_name' && +idconvert '$input_name' #if str($to_format) == 'pep.xml': --pepXML #elif str($to_format) == 'text': --text #end if ---outdir outdir -&& cp outdir/* $output +--outdir 'outdir' +&& cp outdir/* '$output' ]]> </command> <inputs> @@ -49,40 +48,40 @@ <option value="pep.xml">pepXML (pepxml)</option> <option value="text">text</option> </param> - </inputs> - <outputs> - <data format="mzid" name="output" label="${from.input.name.rsplit('.',1)[0]}.${to_format}"> - <change_format> - <when input="to_format" value="pep.xml" format="pepxml" /> - <when input="to_format" value="text" format="txt" /> - </change_format> - </data> - </outputs> - <tests> - <test> - <param name="input" value="Rpal_01.pepXML" /> - <param name="from_format" value="pepxml" /> - <param name="to_format" value="mzid" /> - <output name="output_psms"> - <assert_contents> - <has_text text="MzIdentML" /> - <has_text text="VIKKSTTGRVLSDDILVIRKGEIAARNASHKMR" /> - </assert_contents> - </output> - </test> - <test> - <param name="input" value="Rpal_01.mzid" /> - <param name="from_format" value="mzid" /> - <param name="to_format" value="pep.xml" /> - <output name="output_psms"> - <assert_contents> - <has_text text="msms_pipeline_analysis" /> - <has_text text="VIKKSTTGRVLSDDILVIRKGEIAARNASHKMR" /> - </assert_contents> - </output> - </test> - </tests> - <help> + </inputs> + <outputs> + <data format="mzid" name="output" label="${from.input.name.rsplit('.',1)[0]}.${to_format}"> + <change_format> + <when input="to_format" value="pep.xml" format="pepxml" /> + <when input="to_format" value="text" format="txt" /> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="input" value="Rpal_01.pepXML" /> + <param name="from_format" value="pepxml" /> + <param name="to_format" value="mzid" /> + <output name="output"> + <assert_contents> + <has_text text="MzIdentML" /> + <has_text text="VIKKSTTGRVLSDDILVIRKGEIAARNASHKMR" /> + </assert_contents> + </output> + </test> + <test> + <param name="input" value="Rpal_01.mzid" /> + <param name="from_format" value="mzid" /> + <param name="to_format" value="pep.xml" /> + <output name="output"> + <assert_contents> + <has_text text="msms_pipeline_analysis" /> + <has_text text="VIKKSTTGRVLSDDILVIRKGEIAARNASHKMR" /> + </assert_contents> + </output> + </test> + </tests> + <help> <![CDATA[ idconvert [options] [filemasks] Convert mass spec identification file formats. @@ -118,6 +117,8 @@ idconvert mascot.mzid --pepXML ]]> - </help> - <expand macro="citations" /> + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btn323</citation> + </citations> </tool> |
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| diff -r 9e6e840d6b52 -r edb33e8224c6 msconvert_macros.xml --- a/msconvert_macros.xml Mon Aug 08 10:43:52 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,675 +0,0 @@\n-<macros>\n- <xml name="generic_requirements">\n- <requirements>\n- <requirement type="package" version="3.0.9016">proteowizard</requirement>\n- </requirements>\n- </xml>\n- <token name="@VERSION@">3.0</token>\n- \n- <xml name="msconvertCommand">\n- <command interpreter="python">\n-<![CDATA[\n- #import re\n- #set $ext = $input.ext\n- msconvert_wrapper.py\n- #if $ext == \'wiff\':\n- #set basename = \'absciex\'\n- #if hasattr($input, \'display_name\')\n- #set basename = $re.sub(\'\\W\',\'_\',$input.display_name)\n- #end if\n- --input=${input.extra_files_path}/wiff\n- --input_name=\'${basename}.wiff\n- --implicit=${input.extra_files_path}/wiff_scan\n- --input=${input.extra_files_path}/wiff_scan\n- --input_name=\'${basename}.wiff.scan\n- #else\n- --input=${input}\n- #if hasattr($input, \'display_name\')\n- --input_name=\'${input.display_name}\'\n- #end if\n- #end if\n- --output=${output}\n- ## BEGIN_VERSION_DEFAULT\n- --fromextension=$ext\n- ## END_VERSION_DEFAULT\n- --toextension=${output_type}\n-\n- ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!)\n- #if $data_processing.precursor_refinement.use_mzrefinement\n- #set $input_ident_name = $re.sub(\'\\W\',\'_\',$data_processing.precursor_refinement.input_ident.display_name)\n- #if $data_processing.precursor_refinement.input_ident.ext == \'mzid\':\n- #set $input_ident_name = $re.sub(\'(?i)([.]?mzid)*$\',\'.mzid\',$input_ident_name)\n- #elif $data_processing.precursor_refinement.input_ident.ext == \'pepxml\':\n- #set $input_ident_name = $re.sub(\'(?i)([.]?pep[.]?xml)*$\',\'.pep.xml\',$input_ident_name)\n- #end if\n- --ident=$data_processing.precursor_refinement.input_ident\n- --ident_name=$input_ident_name\n- --refinement=$output_refinement\n- --filter "mzRefiner $input_ident_name\n- msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels\n- thresholdScore=$data_processing.precursor_refinement.thresholdScore\n- thresholdValue=$data_processing.precursor_refinement.thresholdValue\n- thresholdStep=$data_processing.precursor_refinement.thresholdStep\n- maxSteps=$data_processing.precursor_refinement.thresholdMaxSteps"\n- #end if\n-\n- #if $data_processing.peak_picking.pick_peaks\n- --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels"\n- #end if\n-\n- #if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "predictor"\n- --filter "chargeStatePredictor\n- overrideExistingCharge=$data_processing.charge_state_calculation.predictor_overrideExistingCharge\n- minMultipleCharge=$data_processing.charge_state_calculation.minMultipleCharge\n- maxMultipleCharge=$data_processing.charge_state_calculation.maxMultipleCharge\n- singleChargeFractionTIC=$data_processing.charge_state_calculation.singleChargeFractionTIC\n- maxKnownCharge=$data_processing.charge_state_calculation.maxKnownCharge"\n- #else if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "turbocharger"\n- --filter "turbocharger\n- minCharge=$data_processing.charge_state_calculation.minCharge\n- maxCharge=$data_processing.charge_state_calculation.maxCharge\n- precursorsBefore=$data_processing.charge_state_calculation.precursorsBefore\n- precursorsAfter=$data_processing.charge_state_calculation.precursorsAfter\n- halfIsoWidth=$data_processing.charge_state_calculation.halfIsoWidth\n- defaultMinCharge=$data_processing.charge_state_calculation.defaultMinCharge\n- defaultMaxCharge=$data_processing.charge_state_calculation.defaultMaxCharge"\n- #end if\n-\n- #for threshold_entry in $data_processing.thresholds\n- --filter "threshold $threshold_entry.threshold_type $thres'..b'e="mzML" />\n- <param name="activation" value="CID" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-activation.mzML" />\n- </test>\n- <test>\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n- <param name="output_type" value="mzML" />\n- <param name="indices_0|from" value="2" />\n- <param name="indices_0|to" value="4" />\n- <param name="indices_1|from" value="10" />\n- <param name="indices_1|to" value="10" />\n- <param name="indices_2|from" value="13" />\n- <param name="indices_2|to" value="15" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-index-filter.mzML" />\n- </test>\n- <test>\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n- <param name="output_type" value="mzML" />\n- <param name="strip_it" value="true" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-strip-it.mzML" />\n- </test>\n- <test>\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n- <param name="output_type" value="mzML" />\n- <param name="do_ms_level_filter" value="true" />\n- <param name="ms_level_from" value="2" />\n- <param name="ms_level_to" value="2" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-ms-level-filter.mzML" />\n- </test>\n- <test>\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n- <param name="output_type" value="mzML" />\n- <param name="polarity" value="positive" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-polarity-filter.mzML" />\n- </test>\n- <test>\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n- <param name="output_type" value="mzML" />\n- <param name="analyzer" value="IT" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-analyzer-filter.mzML" />\n- </test>\n- <test>\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n- <param name="output_type" value="mzML" />\n- <param name="scan_numbers_0|from" value="3" />\n- <param name="scan_numbers_0|to" value="5" />\n- <param name="scan_numbers_1|from" value="11" />\n- <param name="scan_numbers_1|to" value="11" />\n- <param name="scan_numbers_2|from" value="14" />\n- <param name="scan_numbers_2|to" value="16" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-index-filter.mzML" /> <!-- the scan numbers here produce the same output as the index test above -->\n- </test>\n- <!--<test>\n- <param name="input" value="small.mzML" />\n- <param name="output_type" value="mzML" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-deisotope-poisson.mzML" />\n- </test>-->\n- </xml>\n- <xml name="msconvert_help">\n-**What it does**\n-\n-Allows interconversion within various mass spectrometry peak list formats. Additional options such as filtering and/or precursor recalculation are available.\n-\n-You can view the original documentation here_.\n-\n-.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html\n- </xml>\n-\n- <xml name="citations">\n- <citations>\n- <citation type="doi">10.1093/bioinformatics/btn323</citation>\n- <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},\n- year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->\n- </citations>\n- </xml>\n-\n-</macros>\n' |
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| diff -r 9e6e840d6b52 -r edb33e8224c6 tool_dependencies.xml --- a/tool_dependencies.xml Mon Aug 08 10:43:52 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="proteowizard" version="3.0.9016"> - <repository changeset_revision="e9ae8f0be737" name="package_proteowizard_3_0_9016" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |